AB0002 ATTEMPTS TO LINK EXONIC GENE POLYMORPHISMS TO ANKYLOSING SPONDYLITIS (AS)- ASSOCIATED PROTEIN MODIFIED FUNCTIONALITY: A STRUCTURAL BIOLOGY APPROACH
Authors: E. Eliopoulos, G. Goulielmos, M. Zervou
Journal: Annals of the Rheumatic Diseases (2022)

Background Genome wide association studies (GWAS) have played a primary role in depicting genetic contributions to ankylosing spondylitis (AS) development, while accommodating the exonic polymorphisms on the protein structure level, when available, enhances our understanding of protein function modification. AS is a polygenic disorder and it is the archetype of a group of inflammatory conditions known as spondyloarthropathies because of their tendency to involve the spine [1]. Linking human genetics with therapeutic targets requires understanding of the biological function and structure of the expressed protein by the causal gene variant to be known. Objectives We sought to investigate recently identified AS-associated functional gene polymorphisms, such as ERAP1 , PON1 , CARD9 and JARID1A [2-5] by correlation to protein structure and function. Methods The experimental 3D model structures of the human ERAP1, PON1, CARD9 and JARID1A proteins were used for the localization of the polymorphisms under study. Molecular mechanics/dynamics studies were applied to determine the impact of the polymorphisms on the structural stability of the enzyme and the conformational changes caused were structurally analyzed. The mutants were constructed using molecular modeling with the program MOΕ (Molecular Operating Environment V.2019.01, Chemical Computing HPC), which was also used to analyze the conformational changes caused by the mutation. All figures depicting 3D models were created using the molecular graphics program PyMOL V.2.2 [6]. Results ERAP1 plays a role in trimming peptides for optimal binding to MHC1 molecules by utilizing a complex catalytic mechanism. High resolution structures of ERAP1 have shown that K528 and Q730 are located distal from the active site of the enzyme (Figure 1a). Recent enzymatic and computational studies have demonstrated that the presence of Lys or Arg at position 528 and of glutamine or glutamic acid in position 730 affects differently the conformational distribution of the protein ensemble by altering the conformational plasticity of the enzyme and, therefore, indirectly affecting dissimilarly its activity [7]. The PON1 rs662 (Gln192Arg) variant affects stability and recognition of the ligand recognition site and plays a functional role in inflammatory disorders (Figure 1b). The caspase recruitment domain (CARD) interaction of CARD9 with Bcl10 promotes downstream activation of factors including NF-κB and the mitogen activated protein kinase (MAPK) p38 [8]. The CARD9 rs4077515 (Ser12Asn) variant affects the conformational flexibility of the interacting N-terminal [9] (Figure 1c). JARID1A gene codes for lysine demethylase 5A (KDM5A) a histone demethylase that specifically demethylates ‘Lys-4’ of histone H3. The JARID1A rs11062385 (Met865Thr) SNP that is strongly correlated with expression has been associated with a protective role for the disease but is located in a region of the KMD5A protein with an undefined yet function. Figure 1. The structures of huERAP1 (a), huPON1 (b) and huCARD9 (c) with the mutations highlighted and labeled Conclusion Based on several examples, we have tried to define a rational link from AS-associated gene polymorphisms to structure and to modified function, including metagenomic analysis of SNPs, protein crystallography, protein molecular modeling, molecular mechanics and dynamics. Locating, shaping and understanding the target protein interaction interface plays a decisive role in most cases and provides clues for further pharmacological or medical actions. References [1]Braun and Sieper (2007). Lancet 369:1379–90 [2]Burton et al (2007). Nat Genet 39:1329–37 [3]Xu and Qu (2017). Medicine (Baltimore) 96:e7416 [4]Pointon et al (2010). Genes Immun 11:490-6 [5]Pointon et al (2011). Genes Immun 12:395-8 [6]Schrödinger LLC: The PyMOL Molecular Graphics System 2016 version 2.2) [7]Stamogiannos et al (2015). Mol Immunol 56:1546-58 [8]Holliday et al (2019). Nature Comm 10:3070 [9]Holliday et al (2018). J Biol Chem 293:16803-17 Disclosure of Interests None declared